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Apache Taverna

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Apache Taverna
Developer(s)Apache Software Foundation (myGrid for 2.x)
Stable release
2.5 / April 16, 2014 (2014-04-16)
Repository
Written inJava
Operating systemLinux, Mac OS X, Microsoft Windows
TypeScientific workflow system
LicenseApache License 2.0 (LGPL for 2.x)
Websitetaverna.incubator.apache.org

Apache Taverna is an open source software tool for designing and executing workflows, initially created by the myGrid project under the name Taverna Workbench, now a project under the Apache incubator. Taverna allows users to integrate many different software components, including WSDL SOAP or REST Web services, such as those provided by the National Center for Biotechnology Information, the European Bioinformatics Institute, the DNA Databank of Japan (DDBJ), SoapLab, BioMOBY and EMBOSS. The set of available services is not finite and users can import new service descriptions into the Taverna Workbench.[1][2][3][4][5][6][7][8]

Taverna Workbench provides a desktop authoring environment and enactment engine for scientific workflows. The Taverna workflow engine is also available separately, as a Java API, command line tool or as a server.

Taverna is used by users in many domains, such as bioinformatics,[9][10] cheminformatics,[11] medicine, astronomy,[12] social science, music, and digital preservation.[13]

Some of the services for the use in Taverna workflows can be discovered through the BioCatalogue - a public, centralised and curated registry of Life Science Web services. Taverna workflows can also be shared with other people through the myExperiment social web site for scientists. BioCatalogue and myExperiment are another two product from the myGrid consortium.

Taverna is used in over 350 organizations around the world, both academic and commercial. As of 2011, there have been over 80,000 downloads of Taverna across different versions.

Capabilities

Taverna workflows can invoke general SOAP/WSDL or REST Web services, and more specific SADI, BioMart, BioMoby and SoapLab Web services. It can also invoke R statistical services, local Java code, external tools on local and remote machines (via ssh), do XPath and other text manipulation, import a spreadsheet and include sub-workflows.

Taverna Workbench includes the ability to monitor the running of a workflow and to examine the provenance of the data produced, exposing details of the workflow run as a W3C PROV-O RDF provenance graph,[14] within a structured Research Object bundle[15] ZIP file that includes inputs, outputs, intermediate values and the executed workflow definition.[16]

Taverna includes the ability to search for services described in BioCatalogue to invoke from workflows. However, services do not need to be described within BioCatalogue to be included in workflows as they can be added from a WSDL Web Service description or entered as a REST URI pattern.

Taverna also includes the capability to search for workflows on myExperiment. The Taverna Workbench can download, modify and run workflows discovered on myExperiment, and also upload created workflows in order to share them with others using the social aspects of myExperiment.

Taverna workflows do not need to be executed within the Taverna Workbench. Workflows can also be run by:

  • a command line execution tool
  • remote execution server that allow Taverna workflows to be run on other machines, on computational grids, clouds, from Web pages and portals
  • online workflow designer and enactor OnlineHPC

Taverna allows pipelining and streaming of data.[17] This means that services downstream in the workflow can start as soon as the first data item is received, without waiting for the whole data list to become available from upstream services and iterations. Taverna services execute in parallel when possible, as Taverna workflows are primarily data-driven rather than control-driven.[18]

Taverna Workbench 2.1 splash screen

Extensibility

Taverna allows developers to plugin new functionality and also to use Taverna within their own products. Taverna has been extended to allow additional components within workflows, for example those from the Chemistry Development Kit, SADI semantic Web services, and caGrid. It has also been bundled with other products, for example the Taverna-LC plugin for OpenOffice Calc allows calling services as spreadsheet functions.

Various projects and institutions have run Taverna workflows on grids or have used Taverna to access services on grids, such as KnowARC, NGS (National Grid Service), EGEE (Enabling Grids for E-sciencE) and caGrid.

External tools can be included within Taverna workflows either scripts such as Java Beanshell, though the use of an API Consumer service that generates services for the methods exposed by the tool written in Java or via external tools plugin, which allows users to run tools on a grid or remote/local machine using grid or ssh authentication.

Open source community

Taverna has been an open-source project since 2003,[19] with contributors from multiple academic and industry institutions. In 2014-10, Taverna became an independent Apache incubator project,[20] and changed name to Apache Taverna (incubating). The project is developing Apache Taverna 3.x,[21] which license change from LGPL 2.1 to Apache License 2.0.

References

  1. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1109/CCGRID.2008.17, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1109/CCGRID.2008.17 instead.
  2. ^ Li, P.; Castrillo, J. I.; Velarde, G.; Wassink, I.; Soiland-Reyes, S.; Owen, S.; Withers, D.; Oinn, T.; Pocock, M. R.; Goble, C. A.; Oliver, S. G.; Kell, D. B. (2008). "Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data". BMC Bioinformatics. 9: 334. doi:10.1186/1471-2105-9-334. PMC 2528018. PMID 18687127.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  3. ^ Oinn, T.; Addis, M.; Ferris, J.; Marvin, D.; Senger, M.; Greenwood, M.; Carver, T.; Glover, K.; Pocock, M. R.; Wipat, A.; Li, P. (2004). "Taverna: A tool for the composition and enactment of bioinformatics workflows". Bioinformatics. 20 (17): 3045–3054. doi:10.1093/bioinformatics/bth361. PMID 15201187.
  4. ^ Oinn, T.; Greenwood, M.; Addis, M.; Alpdemir, M. N.; Ferris, J.; Glover, K.; Goble, C.; Goderis, A.; Hull, D.; Marvin, D.; Li, P.; Lord, P.; Pocock, M. R.; Senger, M.; Stevens, R.; Wipat, A.; Wroe, C. (2006). "Taverna: Lessons in creating a workflow environment for the life sciences". Concurrency and Computation: Practice and Experience. 18 (10): 1067–1100. doi:10.1002/cpe.993.
  5. ^ Hull, D.; Wolstencroft, K.; Stevens, R.; Goble, C. A.; Pocock, M. R.; Li, P.; Oinn, T. (2006). "Taverna: A tool for building and running workflows of services". Nucleic Acids Research. 34 (Web Server issue): W729–W732. doi:10.1093/nar/gkl320. PMC 1538887. PMID 16845108. Open access icon
  6. ^ Kawas, E.; Senger, M.; Wilkinson, M. D. (2006). "BioMoby extensions to the Taverna workflow management and enactment software". BMC Bioinformatics. 7: 523. doi:10.1186/1471-2105-7-523. PMC 1693925. PMID 17137515.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  7. ^ Sroka, J.; Kaczor, G.; Tyszkiewicz, J.; Kierzek, A. (2006). "XQTav: An XQuery processor for Taverna environment". Bioinformatics. 22 (10): 1280–1281. doi:10.1093/bioinformatics/btl101. PMID 16551662.
  8. ^ Wolstencroft, K.; Haines, R.; Fellows, D.; Williams, A.; Withers, D.; Owen, S.; Soiland-Reyes, S.; Dunlop, I.; Nenadic, A.; Fisher, P.; Bhagat, J.; Belhajjame, K.; Bacall, F.; Hardisty, A.; Nieva De La Hidalga, A.; Balcazar Vargas, M. P.; Sufi, S.; Goble, C. (2013). "The Taverna workflow suite: Designing and executing workflows of Web Services on the desktop, web or in the cloud". Nucleic Acids Research. 41 (Web Server issue): W557–W561. doi:10.1093/nar/gkt328. PMC 3692062. PMID 23640334.
  9. ^ Stevens, R. D.; Robinson, A. J.; Goble, C. A. (2003). "MyGrid: Personalised bioinformatics on the information grid". Bioinformatics. 19: i302–i304. doi:10.1093/bioinformatics/btg1041. PMID 12855473.
  10. ^ Stevens, R. D.; Tipney, H. J.; Wroe, C. J.; Oinn, T. M.; Senger, M.; Lord, P. W.; Goble, C. A.; Brass, A.; Tassabehji, M. (2004). "Exploring Williams-Beuren syndrome using myGrid". Bioinformatics. 20: i303–i310. doi:10.1093/bioinformatics/bth944. PMID 15262813.
  11. ^ Truszkowski, A.; Jayaseelan, K.; Neumann, S.; Willighagen, E. L.; Zielesny, A.; Steinbeck, C. (2011). "New developments on the cheminformatics open workflow environment CDK-Taverna". Journal of Cheminformatics. 3: 54. doi:10.1186/1758-2946-3-54. PMC 3292505. PMID 22166170.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  12. ^ Hook, R. N.; Romaniello, M.; Ullgrén, M.; Järveläinen, P.; Maisala, S.; Oittinen, T.; Savolainen, V.; Solin, O.; Tyynelä, J.; Peron, M.; Izzo, C.; Licha, T. (2008). "ESO Reflex: A Graphical Workflow Engine for Running Recipes". The 2007 ESO Instrument Calibration Workshop. ESO Astrophysics Symposia European Southern Observatory. p. 169. doi:10.1007/978-3-540-76963-7_23. ISBN 978-3-540-76962-0.
  13. ^ Raditsch, M.; Schlarb, S.; Møldrup-Dalum, P.; Medjkoune, L. (2012). "Web content executable workflows for experimental execution" (PDF).{{cite web}}: CS1 maint: multiple names: authors list (link)
  14. ^ Belhajjame, K.; Zhao, J.; Garijo, D.; Garrido, A.; Soiland-Reyes, S.; Alper, P.; Corcho, O. (2013). "A workflow PROV-corpus based on taverna and wings". Proceedings of the Joint EDBT/ICDT 2013 Workshops on - EDBT '13. p. 331. doi:10.1145/2457317.2457376. ISBN 9781450315999.
  15. ^ Soiland-Reyes, S; Gamble, M; Haines, R (2014-11-05). "Research Object Bundle 1.0" (Specification). researchobject.org. Zenodo. doi:10.5281/zenodo.12586. Retrieved 28 January 2015.
  16. ^ Soiland-Reyes, S; Nenadic, A (2014-10-21). "taverna-prov: Structure of exported provenance". GitHub. Archived from the original on 2014-10-21. Retrieved 28 January 2015.
  17. ^ "Implicit iteration". Taverna 2.5 User Manual. myGrid. 2014-09-09. Retrieved 28 January 2015.
  18. ^ Soiland-Reyes, Stian (2010-12-13). "Parallel service invocations". The Taverna Knowledge Blog. knowledgeblog.org. Retrieved 28 January 2015.
  19. ^ Soiland-Reyes, S; Sufi, S; Seaborne, S (2014-09-23). "Taverna Proposal". Incubator Wiki. Apache Software Foundation. Retrieved 28 January 2015.
  20. ^ "Taverna Project Incubation Status". Apache Incubator. Apache Software Foundation. Retrieved 28 January 2015.
  21. ^ "Download Apache Taverna". Apache Software Foundation. Retrieved 28 January 2015.
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